1. Information

This dataset has 33 different proteins. 20 proteins have at least one glycoforms detected, while 13 do not have any glycoforms.

Five Proteins have calibration curves. They are Clus, ApoC1, ApoA1, ApoD, and ApoE. The calculated calibration curve parameters are below:

2. Calibration Curves

2.1. Clus

This calibration curve has a decent \(R^2\) value.

Calculated calibration parameters:

  • slop: 6.544424810^{6}
  • intercept: -2.726860110^{4}

"The dataset only has one CLUS peptide, QuantPep-CLUS_ASSIIDELFQDR Results, which ranges from 867.9513116 to 7419.8085748, that is perfectly in the range of the calibration curve.

2.2. ApoC1

This curve has a great \(R^2\), with the calculated parameters:

  • slop: 2.046971210^{7}
  • intercept: -1.061018110^{5}

There is also only one ApoC1, pep-APOC1-QSELSAK Results, ranges from 1929.9715452 to 4.830865110^{5}. There seems to be one person with an extreme high value.

2.3. ApoA1

The ApoA1 curve does not seem to be very ideal. The calculated parameters are blow:

  • slop: 1.060068810^{6}
  • intercept: -1.703487210^{4}

There are two ApoA1 peptides:

  • pep-APOA1_LAEYHAK Results, ranges from 4.155885510^{5} to 2.418370310^{6}
  • QuantPep-APOA1_DLATVYVDVLK Results, ranges from 1.223072410^{5} to 5.346366710^{6}

Both the peptides are in a range that is higher than the highest point of the calibration curve.

2.4. ApoD

This calibration curve is perfect.

  • slop: 3.712347710^{7}
  • intercept: -5071.2726236

The ApoD peptide, QuantPep-APOD_VLNQELR Results, ranges from 1.003524910^{5} to 7.600105310^{5}

2.5. ApoE

The ApoE calibration curve is also perfect. The parameters are:

  • slop: 1.091949210^{7}
  • intercept: -2804.97715

Three ApoE peptides are found from the dataset:

  • pep-APOE_LGPLVEQGR_z3 Results， ranges from 6941.3588049 to 3.004544310^{5}
  • pep-APOE_LGPLVEQGR_z4 Results， ranges from 6816.4719865 to 2.901641310^{5}
  • APOE_AATVGSLAGQPLQER_z2 Results, ranges from 1696.1124313 to 7.50223710^{4}

3. Missing Values

Unglycosylated Peptides

The graph below shows the number of zeros in each unglycosylated peptide.

The peptide with 21 zero is APOM_135_ungly_z3 Results. Fortunately the other two APOM peptdies do not have any zero

##     APOM_135_ungly_z3 Results    pep-APOM_SLTSCLDSK Results 
##                            21                             0 
## QuantPep-APOM_AFLLTPR Results 
##                             0

The peptide with 13 zero is APOC3_94A_ungly_z2 Results. And again, the other APOC3 peptdies do not have any zero.

##              APOC3_94A_ungly_z2 Results 
##                                      13 
## QuantPep-APOC3_DALSSVQESQVAQQAR Results 
##                                       0 
##           pep-APOC3_GWVTDGFSSLK Results 
##                                       0

The peptide with 6 zero is LCAT_PVILVPGCLGNQLEAK_z2 Results. And the other LCAT peptdies do not have any zero.

##        LCAT_LEPGQQEEYYR_z2 Results pep-LCAT_SSGLVSNAPGVQIR_z2 Results 
##                                  0                                  0 
##   LCAT_PVILVPGCLGNQLEAK_z2 Results 
##                                  6

The peptide with 3 zero is pep-APOA_NPDAVAAPYCYTR_z2 Results.

##                 pep-APOA1_LAEYHAK Results 
##                                         0 
##           pep-APOA2_SKEQLTPLIK_z2 Results 
##                                         0 
##            pep-APOA4_LAPLAEDVR_z2 Results 
##                                         0 
##            APOA4_LGEVNTYAGDLQK_z2 Results 
##                                         0 
##         pep-APOA_NPDAVAAPYCYTR_z2 Results 
##                                         3 
##        QuantPep-APOA1_DLATVYVDVLK Results 
##                                         0 
## pep-APOA5_AQLLGGVDEAWALLQGLQSR_z3 Results 
##                                         1 
##   APOA2_AGTELVNFLSYFVELGTQPATQ_z2 Results 
##                                         0

The two peptdies with 2 zerois are:

## [1] "pep-APOA5_AQLLGGVDEAWALLQGLQSR_z3 Results"
## [2] "APOL1_LTDVAPVSFFLVLDVVYLVYESK_z2 Results"

Both ApoA5 and APOL1 have only one unglycosylated peptide detected, and neither of them have any glycoforms.

Glycoforms

  1. Peptides with more than 2 zeros will be removed.

  2. Glycans with 6 or more zeros will be removed.

  3. For the rest glycans, zeros will be filled with the lowest value in all samples devided by 2.

  4. Glycans will be normalized to its unglycosylated peptide.

4. Peptides

5. Summary

  1. Many proteins have multiple peptides reported. Which peptide should we used to report the “abundance” of the particular protein? Should we use the one with the highest response (intensity)?

  2. Which peptide should we use to calculate the concentration with the calibration curves?

  3. The ApoA1 curve does not seem to be ideal